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116 dependabot tests failing for python38 #119

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merged 10 commits into from
Apr 10, 2024
Merged

116 dependabot tests failing for python38 #119

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406cbc3
Pinning the jsonshema dependency to see why the tests for pythong > 3…
Apr 9, 2024
6f1458e
Removing references to python 3.8 in the documentation.
Apr 9, 2024
ef8c95e
Updating the dependencies to stop the docs from breaking. This is due…
Apr 9, 2024
bcf111d
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 9, 2024
87279ff
Adding tests for python 3.12 and removing references to the backend i…
Apr 9, 2024
d897b8f
Fixing the lammps versions so that they are compatible with the pytho…
Apr 9, 2024
79456e3
Removing tests for python3.12 as lammps does not have release candida…
Apr 10, 2024
35fbe98
Changing the lammps versions available for installation
Apr 10, 2024
dc8477f
Changing codecov action to v2 to see if it solves the issue with the …
Apr 10, 2024
1e84f30
Bumping the version of the codecov action as this is not solving the …
Apr 10, 2024
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24 changes: 10 additions & 14 deletions .github/workflows/cd.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v4.5.0
with:
python-version: "3.8"
python-version: "3.9"
- name: Make sure virtualevn>20 is installed, which will yield newer pip and possibility to pin pip version.
run: pip install "virtualenv>20"
- name: Install Tox
Expand All @@ -29,26 +29,22 @@ jobs:
fail-fast: false
matrix:
include:
- python-version: "3.8"
lammps-version: "2020.12.24"
backend: django
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I think you can remove all the other backend occurrences. The difference between django/sqlalchemy was removed in AiiDA v2, it no longer makes sense.

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Great! thanks, I suspected it just was not sure why it was there in the latest release.

- python-version: "3.8"
lammps-version: "2020.12.24"
backend: sqlalchemy
- python-version: "3.9"
lammps-version: "2020.12.24"
backend: django
- python-version: "3.9"
lammps-version: "2022.06.23"
- python-version: "3.10"
lammps-version: "2021.09.29"
backend: django
lammps-version: "2022.06.23"
- python-version: "3.11"
lammps-version: "2022.06.23"

runs-on: ubuntu-latest

services:
postgres:
image: postgres:12
env:
POSTGRES_DB: test_${{ matrix.backend }}
POSTGRES_DB: test
POSTGRES_PASSWORD: ""
POSTGRES_HOST_AUTH_METHOD: trust
options: >-
Expand Down Expand Up @@ -86,7 +82,7 @@ jobs:
tox -e ${{ matrix.python-version }}-aiida_lammps -- tests/ --cov=./aiida_lammps --cov-append --cov-report=xml --cov-report=term-missing

- name: Upload to Codecov
if: matrix.python-version == 3.8
if: matrix.python-version == 3.10
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
Expand All @@ -102,10 +98,10 @@ jobs:
steps:
- name: Checkout source
uses: actions/checkout@v3.3.0
- name: Set up Python 3.8
- name: Set up Python 3.9
uses: actions/setup-python@v4.5.0
with:
python-version: "3.8"
python-version: "3.9"
- name: install flit
run: |
pip install flit~=3.4
Expand Down
14 changes: 6 additions & 8 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ jobs:
- name: Set up Python
uses: actions/setup-python@v4.5.0
with:
python-version: "3.8"
python-version: "3.9"
- name: Make sure virtualevn>20 is installed, which will yield newer pip and possibility to pin pip version.
run: pip install "virtualenv>20"
- name: Install Tox
Expand All @@ -28,16 +28,14 @@ jobs:
fail-fast: false
matrix:
include:
- python-version: "3.8"
lammps-version: "2020.03.03"
- python-version: "3.8"
lammps-version: "2020.12.24"
- python-version: "3.9"
lammps-version: "2020.12.24"
- python-version: "3.9"
lammps-version: "2020.03.03"
lammps-version: "2022.06.23"
- python-version: "3.10"
lammps-version: "2021.09.29"
lammps-version: "2022.06.23"
- python-version: "3.11"
lammps-version: "2022.06.23"

runs-on: ubuntu-latest

Expand Down Expand Up @@ -87,7 +85,7 @@ jobs:
tox -e ${{ matrix.python-version }}-aiida_lammps -- tests/ --cov=./aiida_lammps --cov-append --cov-report=xml --cov-report=term-missing

- name: Upload to Codecov
if: matrix.python-version == 3.8
if: matrix.python-version == 3.10
uses: codecov/codecov-action@v3
with:
token: ${{ secrets.CODECOV_TOKEN }}
Expand Down
5 changes: 3 additions & 2 deletions docs/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,10 +4,11 @@
`tox -e docs-clean` and `tox -e docs-update`,
or directly: `sphinx-build -n -W --keep-going docs/source docs/_build`
"""

import pathlib
import time

from aiida.manage.configuration import load_documentation_profile
from aiida.manage.configuration import Profile, load_profile

from aiida_lammps import __version__

Expand All @@ -16,7 +17,7 @@
# Load the dummy profile even if we are running locally, this way the
# documentation will succeed even if the current
# default profile of the AiiDA installation does not use a Django backend.
load_documentation_profile()
load_profile(Profile("docs", {"process_control": {}, "storage": {}}))

project = "AiiDA LAMMPS"
copyright = f"2021-{time.localtime().tm_year}, AiiDA Team. All rights reserved"
Expand Down
4 changes: 2 additions & 2 deletions docs/source/developers/index.md
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Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@ The test suite can be run in an isolated, virtual environment using `tox` (see `

```console
pip install tox
tox -e 3.8-aiida_lammps
tox -e 3.9-aiida_lammps
```

or directly:
Expand All @@ -57,7 +57,7 @@ conda install lammps==2019.06.05
You can specify a different executable name for LAMMPS with:

```console
tox -e 3.8-aiida_lammps -- --lammps-exec lmp_exec
tox -e 3.9-aiida_lammps -- --lammps-exec lmp_exec
```

To output the results of calcjob executions to a specific directory:
Expand Down
33 changes: 17 additions & 16 deletions pyproject.toml
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Expand Up @@ -5,30 +5,34 @@ build-backend = "flit_core.buildapi"
[project]
name = "aiida-lammps"
dynamic = ["version", "description"]
authors = [{name = "Chris Sewell", email = "chrisj_sewell@hotmail.com"}, {name = "Jonathan Chico", email = "jonathan.chico@sandvik.com"}]
authors = [
{ name = "Chris Sewell", email = "chrisj_sewell@hotmail.com" },
{ name = "Jonathan Chico", email = "jonathan.chico@sandvik.com" },
]
readme = "README.md"
license = {file = "LICENSE"}
license = { file = "LICENSE" }
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
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If you add this, maybe also add 3.11 to the test matrix of the CI? Also, please update requires-python to be >=3.9. Finally, do you also want to add 3.12 perhaps? aiida-core supports it

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Hi @sphuber !
Thanks for the comments, I wonder if adding the 3.12 is okay since well the plugin supports it but I have not found a lammps release candidate that can be installed with conda for python 3.12 (in general it is a bit of a pain to see which version of lammps is compatible with which python version since the only way seems to look into the conda wheels)

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Does lammps depend on Python?

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Only on the sense on how we install it, we install lammps using conda in the action, and then we use the same python version for aiida. So if we install install python 3.12 there is no lammps conda release for it.
We could install it in some other way, it is possible to do it via apt, but the versioning is a bit unclear there

"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Chemistry",
"Topic :: Scientific/Engineering :: Physics",
"Framework :: AiiDA"
"Framework :: AiiDA",
]
keywords = ["aiida", "workflows", "lammps"]
requires-python = ">=3.8"
requires-python = ">=3.9"
dependencies = [
"aiida-core[atomic_tools]>=2.0.0,<3.0.0",
"aiida-core[atomic_tools]~=2.3",
"importlib_resources",
"jsonschema",
"jsonschema~=3.2.0",
"numpy",
"packaging",
"python-dateutil"
"python-dateutil",
]

[project.urls]
Expand All @@ -43,7 +47,7 @@ tests = [
"pytest-cov",
"coverage",
"pytest-timeout",
"pytest-regressions"
"pytest-regressions",
]

pre-commit = [
Expand All @@ -62,7 +66,7 @@ docs = [
'sphinxcontrib-details-directive~=0.1.0',
'sphinx-autoapi~=3.0',
'myst_parser~=1.0.0',
"furo"
"furo",
]

[project.entry-points."aiida.calculations"]
Expand All @@ -86,15 +90,12 @@ docs = [
name = "aiida_lammps"

[tool.flit.sdist]
exclude = [
"docs/",
"tests/",
]
exclude = ["docs/", "tests/"]

[tool.coverage.run]
# Configuration of [coverage.py](https://coverage.readthedocs.io)
# reporting which lines of your plugin are covered by tests
source=["aiida_lammps"]
source = ["aiida_lammps"]

[tool.isort]
skip = ["venv"]
Expand All @@ -112,7 +113,7 @@ profile = "black"
[tool.tox]
legacy_tox_ini = """
[tox]
envlist = pre-commit,{3.8,3.9,3.10}-aiida_lammps
envlist = pre-commit,{3.9,3.10,3.11}-aiida_lammps
requires = virtualenv >= 20
isolated_build = True

Expand Down
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